PaperClipAI/doc/DATABASE.md

Database

Paperclip uses PostgreSQL via Drizzle ORM. There are three ways to run the database, from simplest to most production-ready.

1. Embedded PostgreSQL — zero config

If you don't set DATABASE_URL, the server automatically starts an embedded PostgreSQL instance and manages a local data directory.

pnpm dev

That's it. On first start the server:

1. Creates a ~/.paperclip/instances/default/db/ directory for storage
2. Ensures the paperclip database exists
3. Runs migrations automatically for empty databases
4. Starts serving requests

Data persists across restarts in ~/.paperclip/instances/default/db/. To reset local dev data, delete that directory.

If you need to apply pending migrations manually, run:

pnpm db:migrate

When DATABASE_URL is unset, this command targets the current embedded PostgreSQL instance for your active Paperclip config/instance.

Issue reference mentions follow the normal migration path: the schema migration creates the tracking table, but it does not backfill historical issue titles, descriptions, comments, or documents automatically.

To backfill existing content manually after migrating, run:

pnpm issue-references:backfill
# optional: limit to one company
pnpm issue-references:backfill -- --company <company-id>

Future issue, comment, and document writes sync references automatically without running the backfill command.

This mode is ideal for local development and one-command installs.

Docker note: the Docker quickstart image also uses embedded PostgreSQL by default. Persist /paperclip to keep DB state across container restarts (see doc/DOCKER.md).

2. Local PostgreSQL (Docker)

For a full PostgreSQL server locally, use the included Docker Compose setup:

docker compose up -d

This starts PostgreSQL 17 on localhost:5432. Then set the connection string:

cp .env.example .env
# .env already contains:
# DATABASE_URL=postgres://paperclip:paperclip@localhost:5432/paperclip

Run migrations:

DATABASE_URL=postgres://paperclip:paperclip@localhost:5432/paperclip \
  pnpm db:migrate

Start the server:

pnpm dev

3. Hosted PostgreSQL (Supabase)

For production, use a hosted PostgreSQL provider. Supabase is a good option with a free tier.

Setup

1. Create a project at database.new
2. Go to Project Settings > Database > Connection string
3. Copy the URI and replace the password placeholder with your database password

Connection string

Supabase offers two connection modes:

Direct connection (port 5432) — use for migrations and one-off scripts:

postgres://postgres.[PROJECT-REF]:[PASSWORD]@aws-0-[REGION].pooler.supabase.com:5432/postgres

Connection pooling via Supavisor (port 6543) — use for the application:

postgres://postgres.[PROJECT-REF]:[PASSWORD]@aws-0-[REGION].pooler.supabase.com:6543/postgres

Configure

For the application runtime, use a direct PostgreSQL connection unless the database client has explicit prepared-statement configuration for your pooling mode:

DATABASE_URL=postgres://postgres.[PROJECT-REF]:[PASSWORD]@aws-0-[REGION].pooler.supabase.com:5432/postgres

If you later run the app with a pooled runtime URL, set DATABASE_MIGRATION_URL to the direct connection URL. Paperclip uses it for startup schema checks/migrations and plugin namespace migrations, while the app continues to use DATABASE_URL for runtime queries:

DATABASE_URL=postgres://postgres.[PROJECT-REF]:[PASSWORD]@aws-0-[REGION].pooler.supabase.com:6543/postgres
DATABASE_MIGRATION_URL=postgres://postgres.[PROJECT-REF]:[PASSWORD]@aws-0-[REGION].pooler.supabase.com:5432/postgres

If your hosted database requires transaction-pooling-only connections (pgbouncer transaction mode, Supavisor port 6543, Neon -pooler endpoints), set DATABASE_PREPARED_STATEMENTS=false so the client does not rely on session-scoped prepared statements, and keep DATABASE_MIGRATION_URL on a direct connection. Do not edit database client source files as part of deployment setup.

Client tuning (optional)

All of these are optional; when unset, the driver defaults apply and behavior is unchanged — typical self-hosted setups need none of them:

DATABASE_PREPARED_STATEMENTS=false   # required for transaction-mode poolers; default: enabled
DATABASE_POOL_MAX=25                 # connection pool size; default: 10
DATABASE_IDLE_TIMEOUT_SECONDS=60     # close idle pooled connections; default: keep open
DATABASE_CONNECT_TIMEOUT_SECONDS=10  # default: 30

Push the schema

# Use the direct connection (port 5432) for schema changes
DATABASE_URL=postgres://postgres.[PROJECT-REF]:[PASSWORD]@...5432/postgres \
  pnpm db:migrate

Free tier limits

• 500 MB database storage
• 200 concurrent connections
• Projects pause after 1 week of inactivity

See Supabase pricing for current details.

Switching between modes

The database mode is controlled by DATABASE_URL:

DATABASE_URL	Mode
Not set	Embedded PostgreSQL (~/.paperclip/instances/default/db/)
postgres://...localhost...	Local Docker PostgreSQL
postgres://...supabase.com...	Hosted Supabase

Your Drizzle schema (packages/db/src/schema/) stays the same regardless of mode.

Migration authoring checklist

The 0126 issue comment attribution backfill showed the failure mode this checklist is meant to prevent: each batch looked for the next rows with an unindexed predicate, so PostgreSQL repeatedly scanned the same table and the migration became O(n²) as the table grew.

When authoring migrations or one-time backfills:

• Create the supporting index for the batch predicate before the backfill loop runs.
• Bound batches by an indexed key, such as an id range or keyset pagination cursor. Do not use OFFSET pagination or a query shape that re-scans already-visited rows each batch.
• Avoid unbounded full-table UPDATE or DELETE statements. Add a selective predicate and process rows in bounded batches when table size can be large.
• Use CREATE INDEX CONCURRENTLY for large existing tables when the migration can run outside a transaction and must avoid long write locks.
• Split schema changes, index creation, and data backfill into separate phases so each step has clear locking and rollback behavior.
• Treat the check:migrations CI gate as the enforcement backstop for these rules. If it flags a migration, rewrite the migration or add a suppression comment with the indexed predicate, batch bound, and reason the remaining scan is safe.

Migration snapshots

drizzle-kit generate diffs packages/db/src/schema/ against the newest snapshot in packages/db/src/migrations/meta/. That snapshot must describe the schema that every migration produces when they run in order. A snapshot that drifts from the schema makes the next migration wrong, because generate folds the drift into it. The drift can add a column that an earlier migration already created, which makes that migration fail on a fresh database. It can also drop a column that the schema still uses.

• Create every migration with pnpm --filter @paperclipai/db generate. Do not hand-write a snapshot.
• Do not hand-edit a snapshot to resolve a merge conflict. Renumber your migration and run generate again, as packages/db/.gitattributes describes.
• packages/db/src/migration-snapshot-drift.test.ts is the enforcement backstop. It repeats the diff that generate performs and fails when the newest snapshot no longer matches packages/db/src/schema/.

Resource membership tables

Paperclip stores current-user sidebar membership state in:

• project_memberships
• agent_memberships

These rows are company-scoped and user-scoped. A missing row means the user is joined, so existing users keep seeing projects and agents in the sidebar until they explicitly leave them. Rows only control sidebar visibility; they do not affect project/agent detail access, all-pages, selectors, assignment flows, or existing company permissions.

Both tables use a unique key on (company_id, user_id, resource_id) and keep state as joined or left. Join/leave mutations are idempotent board-user /me operations and write activity entries when the effective state changes.

Decision training snapshot retention

decision_training_examples stores a point-in-time copy of an issue, its comments, relevant runs, and the selected decision. Each row carries the scrub_deleted_comments_v1 retention policy marker, and JSONL exports include that marker alongside the snapshot.

• Deleting a captured source comment transactionally replaces that comment in every affected snapshot with a content-free redaction tombstone. The original body, presentation, and metadata are not retained in the training record.
• Deleting an issue deletes its decision-training examples through the issue_id foreign-key cascade.
• Deleting a training example deletes only that example and does not mutate the source issue.

This policy makes training exports self-describing while keeping the decision record usable after a comment deletion without retaining content the author removed.

Decision queues and triage provenance

The decisions desk stores queue membership, decide-by/snooze state, and retention state in decision_queues, decision_queue_items, decision_triage, and decision_retention. These sidecars use the stable attention identity (source_kind, source_id) so all attention source kinds can participate without copying source titles, bodies, projects, or other visibility-sensitive data.

decision_triage_events is append-only history for queue and triage changes. Current rows and history both carry server-derived user/agent, heartbeat run, API-key, and responsible-user attribution where applicable. Queue reads must resolve and authorize their source rows at read time; a sidecar row is never a visibility grant.

Triage writes serialize on the company and attention-source identity so concurrent partial updates preserve both fields and produce monotonic history versions.

decision_retention tracks the last observed source activityAt, Keep, reversible archive provenance, and monotonic source/archive versions. decision_archive_notification_outbox has a unique key over company, source identity, archive version, and immutable origin agent so repeated sweeps cannot enqueue duplicate notifications; delivery claims are retryable and coalesced per agent.

Native runner persistence

Native runner state is additive to the existing heartbeat tables. Every existing heartbeat_runs row defaults to runtime_mode = 'legacy'; adding these columns does not select the native runtime or start a runner process. Native execution can record its resolved runtime profile, provider session, driver, completion contract, durable event cursor, and finalization phase on the run when a later rollout explicitly selects it.

completion_contracts, native_run_results, native_run_finalizations, work_assessments, status_decisions, and status_decision_effects form the append-oriented evidence and status-decision chain. Unique fingerprints, versions, ordinals, and idempotency keys make retries deterministic. Composite foreign keys bind every contract, result, assessment, decision, effect, and finalization to one company, issue, and run. The database rejects mixed-owner evidence even when every referenced ID exists. Native source identities on heartbeat_run_events are nullable so legacy events remain readable without rewriting historical rows. Per-run native source identifiers are unique, while the existing legacy sequence behavior remains unchanged. The hidden native coordinator serializes on its bound heartbeat_runs row, allocates next_event_seq, and commits a validated PRP event before the transport sends its cumulative ACK. Byte-equivalent source retries return the existing cursor; gaps and conflicting replays fail closed. Accepted structured results enter the finalization ledger, whose retry time and owner lease are checked under a row lock. None of these writes selects a runtime or changes a legacy run's execution path.

Issue status_version advances only when status changes. The JavaScript backup path includes user-defined functions and triggers so a restored database keeps that invariant. Removing or disabling a future native rollout flag must not delete these records; persisted experimental runs remain available for recovery and inspection.

Plugin database namespaces

The plugin runtime tracks plugin-owned database namespaces and migrations in plugin_database_namespaces and plugin_migrations. Hosted deployments that separate runtime and migration connections should set DATABASE_MIGRATION_URL; plugin namespace migration work uses the migration connection when present.

Backups

Paperclip supports automatic and manual logical database backups. These dumps include non-system database schemas such as public, the Drizzle migration journal, and plugin-owned database schemas. See doc/DEVELOPING.md for the current paperclipai db:backup / pnpm db:backup commands and backup retention configuration.

Database backups do not include non-database instance files such as local-disk uploads, workspace files, or the local encrypted secrets master key. Back those paths up separately when you need full instance disaster recovery.

Secret storage

Paperclip stores secret metadata and versions in:

• user_secret_definitions
• user_secret_declarations
• company_secrets
• company_secret_versions
• company_secret_bindings
• secret_access_events

Company secrets use company_secrets.scope = 'company' and are bound directly through company_secret_bindings. User-specific secrets reuse the same provider and version storage, but each value is a company_secrets.scope = 'user' row with owner_user_id and user_secret_definition_id set. Definitions describe the reusable company-level slot, declarations record where user_secret_ref bindings are required, and the concrete value is selected later for the responsible user.

Secret-aware env bindings are supported by agents, projects, and routines. Routine env lives in routines.env, is captured in routine_revisions.snapshot, and routine dispatches store routine_runs.routine_revision_id so runtime secret resolution uses the env snapshot that existed when the run was created. Routine secret refs bind with target_type = 'routine', target_id = routines.id, and config_path values under env.*.

For local/default installs, the active provider is local_encrypted:

• Secret material is encrypted at rest with a local master key.
• Default key file: ~/.paperclip/instances/default/secrets/master.key (auto-created if missing).
• CLI config location: ~/.paperclip/instances/default/config.json under secrets.localEncrypted.keyFilePath.
• Backup/restore requires both the database metadata and the local master key file; either artifact alone is insufficient.
• The server best-effort enforces 0600 key file permissions and provider health reports permission warnings.
• User-scoped values use the same local encrypted provider path. Database backups preserve definitions, declarations, owner metadata, version metadata, and access events, but restored user-scoped values are decryptable only when the matching local master key is restored with the database.

Optional overrides:

• PAPERCLIP_SECRETS_MASTER_KEY (32-byte key as base64, hex, or raw 32-char string)
• PAPERCLIP_SECRETS_MASTER_KEY_FILE (custom key file path)

Strict mode to block new inline sensitive env values:

PAPERCLIP_SECRETS_STRICT_MODE=true

You can set strict mode and provider defaults via:

pnpm paperclipai configure --section secrets

Inline secret migration command:

npx paperclipai secrets migrate-inline-env --company-id <company-id> --apply

# direct database maintenance fallback
pnpm secrets:migrate-inline-env --apply

Hosted AWS provider notes live in SECRETS-AWS-PROVIDER.md.